Algorithms for approximate string matching
Information and Control
A fast bit-vector algorithm for approximate string matching based on dynamic programming
Journal of the ACM (JACM)
A guided tour to approximate string matching
ACM Computing Surveys (CSUR)
Approximate String Matching in DNA Sequences
DASFAA '03 Proceedings of the Eighth International Conference on Database Systems for Advanced Applications
Rapid Large-Scale Oligonucleotide Selection for Microarrays
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Fast and Accurate Probe Selection Algorithm for Large Genomes
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Fast and Sensitive Probe Selection for DNA Chips Using Jumps in Matching Statistics
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
YODA: selecting signature oligonucleotides
Bioinformatics
Increased bit-parallelism for approximate and multiple string matching
Journal of Experimental Algorithmics (JEA)
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The accuracy of a DNA microarray is fairly dependent on the quality of the probes it uses; a good probe should be specific for exactly one gene. Most sequence based algorithms use the edit distance to the target sequences as the measure of the specificity of the probe. We propose a novel algorithm for finding gene-specific probes which avoids large amounts of redundant computations of the edit distance, while maintaining the same accuracy as that provided by an exhaustive search. Our approach utilizes the fact that when the starting position of a probe candidate is moved only a few base pairs, the change in the edit distance to the off-target sequence is limited. The proposed algorithm does not use any index structures and is insensitive to the length of the probes. Our approach enables short (20∼30 bases) or long (50 or more bases) probes to be computed for genomes of size 10M within a day.